Using biological entities as an example, it is known that the simple act of naming an entity, which is part of a large, complex classification or taxonomic system, has potentially far-reaching and long-lived consequences. For example, those names ascribed to organisms serve as a primary entry point into the scientific, medical, and technical literature and figure prominently in countless laws and regulations governing various aspects of commerce, public safety and public health. Biological names also serve as a primary entry point into many of the central databases that the scientific community and the general public rely on. While legalistic Codes of Nomenclature exist that govern the formation, assignment, and usage of names to biological taxa, the process of biological classification is not governed by these Codes of Nomenclature. Taxonomies represent the scientific opinions of the individuals who create them, and may be of varying quality or consistency. Hence, legitimate and valid names may be ascribed to poorly-formed taxa and illegitimate and invalid names may be assigned to well-formed and/or correctly identified taxa. Moreover, biological names are neither unique nor permanent. A single organism can bear multiple names (synonyms) that represent differing taxonomic opinions that may have been rendered either in sequence or in parallel. Instances of homonymy also occur, in which a single name may refer to more than one group of organisms that are of markedly different evolutionary lineages (e.g. the genus name Bacillus applies to bacteria and insects). Orthographic variants may also occur, arising from correction of nomenclatural errors.
Those whose work involves bacteria, from research scientists and clinicians to public officials and bioterrorism experts, face an ever-growing list of names for everything from whole organisms to individual genes, proteins, and sub-cellular components. While many bacteria are harmless and others can be beneficial, some are the causative agents of potentially lethal diseases. Knowing which is which requires reasoned judgment and on-demand access to the correct information, information that is typically accessed using a scientific name. With rapid advances in knowledge of the depth and breadth of bacterial diversity, the list of names not only grows, it also undergoes incremental re-definition on a daily basis.
While these additions and name changes are of considerable interest to a relatively small number of experts engrossed in bacterial classification, they present a significant problem to both end-users and information providers, who must invest a significant and increasing effort to make the connections between new names to names in publications that predate any change. Failure to maintain name currency may prevent scientists and non-scientists alike from tracking important developments in their field and may trigger inappropriate or life-threatening responses.
Simply put, the continual rapid change in the nomenclature of bacteria has outstripped the ability of most end-users, information providers, and device manufacturers to keep pace. What is needed is a bacterial name-lookup service that permits on-demand access to the correct information at the point of need, regardless of the name that is used. Ideally, that same service would provide a means of synchronizing updates across the entire field, in the scientific literature and databases, in diagnostic instruments, and wherever else bacterial names must be resolved.
The disjunction between nomenclature and taxonomy leads to an accumulation of dubious names in the literature and databases. While experts in taxonomy and biological nomenclature may be able to recognize and correctly interpret such circumstances, few others have the requisite skills to do so, resulting in frequent misapplication of names and misinterpretation of the taxonomic record. From a practical, legal, or regulatory sense, either incorrect nomenclature or errors in classification or identification can have significant and unintended consequences. For example, these errors may lead to the addition or removal of biological species from lists of tightly-regulated organisms such as those appearing on the CDC list of Restricted Select Agents, those governed by the USDA APHIS program, those covered by the Endangered Species Act, or those restricted by packaging and shipping regulations maintained by the USPS, DOT and various international bodies such as the International Airline Transport Association (IATA). The use of biological names as a means of information retrieval is not reliable as these names are neither unique nor persistent.
The present invention provides systems and methods for automatically enabling digital resources, based on an underlying information architecture, as well as a means of accessing data related to those entities in a networked environment using persistent, globally unique identifiers.
The invention enables efficient mining of enormous amounts of biological literature and annotations relevant to a particular organism, even if the organism has undergone multiple taxonomic re-classifications and renaming. This will prevent the introduction of errors related to semantic inconsistencies as well as loss of information. The present invention “future-proofs” those products to which it is applied by providing a method of persistently linking biological names or other terms found in published content to the expertly managed information about the origins, definition, and current usage of those terms. The present invention can also serve as a fine-grained marketing tool by establishing persistent links between terms and related products for sale. The present invention provides services which assure content providers that their offerings will always be accessible to their end-users and eliminate the burden and costs of tracking and managing rapidly changing biological terminologies.